Tuesday, January 6, 2009

Sequence Unknown Antibodies Fast

If you are wondering why Santa didn't bring you that fast antibody sequencer you asked for...there is a good reason...UC San Diego researchers and their collaborators are still inventing it.

In a paper in the December issue of Nature Biotechnology, the bioinformatics researchers from UC San Diego and Genentech propose a new shotgun protein sequencing method reduces the time required to sequence an unknown antibody to under 36 hours. This is a “dramatic reduction” compared to the most widely used technique today, which can take weeks or even months.

“Our new approach has the potential to be a disruptive technology for all protein sequencing applications,” said Nuno Bandeira, lead author on the paper and director of the new Center for Computational Mass Spectrometry (CCMS) at UC San Diego. “This project is a collaboration with Genentech, the leader in development of antibody-based drugs, and it illustrates the potential impact that this center and this technology can have on the biotech industry in California and around the world.”

Bandeira’s co-authors on the Nature Biotechnology paper include UC San Diego computer science and engineering professor Pavel Pevzner, director of the Calit2-based Center for Algorithmic and Systems Biology (CASB); and three researchers from the Protein Chemistry Department of San Francisco-based Genentech: Victoria Pham, David Arnott, and Jennie R. Lill.